I am using a .fasta file, as required to be the database. I do this by converting my .bam file into a fastq, then into a fasta file using bedtools/or samtools.

The extraction is done by the simple command:

samtools -b -f 4 example.bam > unaligned_example.bam

Then, I index my unalinged_example.bam (using samtools).

Then I create an index for my reference fasta in bowtie2, then I convert my .bam file to a fastq file and run the alignment:

bowtie2 -x index -U unaligned_example.fastq -S mapped.sam

With BLAST+, I do the same but I create a database out of my converted .bam (as mentioned beforehand).

blastn -query example_ref.fasta -db unaligned_example_db -out alignment_results_sbs.txt -outfmt 6

Or with more sensitive specifications:

blastn -query example_ref.fasta -db unaligned_example_db -out alignment_results.txt -outfmt 6 -num_threads 4 -max_target_seqs 100 -word_size 7 -evalue 1e-7 -reward 1 -penalty -3 -gapopen 5 -gapextend 2

Thanks for your help